Align FAA hydrolase family protein (characterized, see rationale)
to candidate 8502215 DvMF_2925 5-carboxymethyl-2-hydroxymuconate Delta-isomerase (RefSeq)
Query= uniprot:A0A2E7P912 (281 letters) >FitnessBrowser__Miya:8502215 Length = 260 Score = 150 bits (379), Expect = 3e-41 Identities = 89/219 (40%), Positives = 121/219 (55%), Gaps = 14/219 (6%) Query: 44 DKIRKLDLESLPAVEGSPRIGACVGNIGKFICIGLNYADHAAESNLPIPAEPVVFNKWTS 103 D I DL LP V S K IC G+NY DHAAE P+P EPV F K + Sbjct: 33 DPIPLADLAILPVVAPS-----------KIICAGMNYRDHAAEIGFPVPDEPVFFLKAPT 81 Query: 104 AVVGPNDDVKIPRGSKKTDWEVELGVVIGKGGSYIDEKDAMSHVAGYCVVNDVSEREYQI 163 AV+G + +P+G + D+E EL +V+G+ I +HV GY NDV+ R+ Q Sbjct: 82 AVIGSGQPILVPQGVGRVDYEGELAIVVGRQCRNISPDAVPAHVFGYTCANDVTARDQQ- 140 Query: 164 ERGGTWDKGKGCDTFGPIGPWLVTRDEVADPQKLGMWLEVDGKRYQNGNTSTMIFGVAHI 223 R G + + KG DTF P+GPW+ T ++ D L + V+G+ Q GNT+ M+F + Sbjct: 141 RRDGLFGRCKGYDTFCPVGPWIET--DLPDTASLAVRTLVNGEVRQQGNTADMLFTPNEM 198 Query: 224 VSYLSRFMSLQPGDVISTGTPPGVGMGVKPEAVYLRAGQ 262 VS +SR M+L PGD+I TGTP GVG V + V + Q Sbjct: 199 VSAISRVMTLLPGDLILTGTPVGVGPIVPGDEVRVEIEQ 237 Lambda K H 0.316 0.138 0.419 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 1 Number of Hits to DB: 230 Number of extensions: 10 Number of successful extensions: 3 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 1 Number of HSP's successfully gapped: 1 Length of query: 281 Length of database: 260 Length adjustment: 25 Effective length of query: 256 Effective length of database: 235 Effective search space: 60160 Effective search space used: 60160 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 42 (22.0 bits) S2: 47 (22.7 bits)
This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.
Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.
A candidate for a step is "high confidence" if either:
Otherwise, a candidate is "medium confidence" if either:
Other blast hits with at least 50% coverage are "low confidence."
Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:
GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).
For more information, see:
If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know
by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory